[med-svn] [Git][med-team/sweed][master] 3 commits: New upstream version 3.2.1+dfsg
Nilesh Patra
gitlab at salsa.debian.org
Thu Aug 27 19:02:20 BST 2020
Nilesh Patra pushed to branch master at Debian Med / sweed
Commits:
6a9062c9 by Nilesh Patra at 2020-08-27T23:27:56+05:30
New upstream version 3.2.1+dfsg
- - - - -
679e0ec1 by Nilesh Patra at 2020-08-27T23:27:57+05:30
Update upstream source from tag 'upstream/3.2.1+dfsg'
Update to upstream version '3.2.1+dfsg'
with Debian dir ec7fb913a04daefd7475168d4c0b44247d543b1c
- - - - -
be1ced6a by Nilesh Patra at 2020-08-27T23:30:52+05:30
Update changelog
- - - - -
3 changed files:
- README.txt
- + SweeD.h~
- debian/changelog
Changes:
=====================================
README.txt
=====================================
=====================================
SweeD.h~
=====================================
@@ -0,0 +1,396 @@
+/*
+ * SweeD
+ *
+ * Copyright September 2012 by Nikolaos Alachiotis and Pavlos Pavlidis
+ *
+ * This program is free software; you may redistribute it and/or modify its
+ * under the terms of the GNU General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option)
+ * any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
+ * or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
+ * for more details.
+ *
+ * For any other enquiries send an email to
+ * Pavlos Pavlidis (pavlidisp at gmail.com) or
+ * Nikolaos Alachiotis (n.alachiotis at gmail.com)
+ *
+ */
+
+
+#ifndef _SweeD_H
+#define _SweeD_H
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <assert.h>
+#include <math.h>
+#include <time.h>
+#include <sys/time.h>
+#include <limits.h>
+
+
+#include "SweeD_BFGS.h"
+
+#ifdef _USE_PTHREADS
+#include <pthread.h>
+#include <unistd.h>
+
+#define EXIT 127
+#define BUSYWAIT 0
+#define LIKSFS 1
+#define COMPRVLUT 2
+#define COMPALPHA 3
+
+#endif
+
+#ifdef _DO_CHECKPOINTS
+#include "dmtcpaware.h"
+#endif
+
+#ifdef _ANALYTICAL_SFS
+#include <mpfr.h>
+#include <float.h>
+#define ACC 10000
+#define APPROX 0
+#define TOLTIME 1e-7
+#define RESCALE 1
+#endif
+
+#define ENTRIES_PER_INT 32
+#define DENOMINATOR_OFFSET 0.00001
+#define REGISTER_WIDTH 32
+#define MAXSIZE 10000
+#define INFILENAMESIZE 1000
+#define SEQNAMESIZE 1000
+#define DECREASE 0.99
+#define MINSNPPERWINDOW 5
+#define STRINGLENGTH 100
+#define VCF_HLENGTH 9 // number of fields in the VCF header line
+#define MAX_CHROM_NAME_VCF 100
+#define MAX_STATES_VCF 5
+
+#define RESULTS_DEFAULT 0
+#define RESULTS_ALL 1
+
+#define RSQUARE 0
+#define DOM 1
+#define ABSDOM 2
+#define JUSTD 3
+#define ABSD 4
+#define ABSDOM2 5
+
+#define ZERO '0'
+#define ONE '1'
+#define GAP '-'
+#define AD 'A'
+#define CY 'C'
+#define GU 'G'
+#define TH 'T'
+#define UN 'N'
+
+#define BINARY 2
+#define BINARY_WITH_GAPS 3
+#define DNA 4
+#define DNA_WITH_GAPS 5
+#define STATESALL 8
+
+#define OTHER_FORMAT -1
+#define MS_FORMAT 0
+#define FASTA_FORMAT 1
+#define MACS_FORMAT 2
+#define VCF_FORMAT 3
+#define SF_FORMAT 4
+
+#define INTOKS 8
+
+#define N_REF 2
+#define N_ALT 3
+#define N_INFO 6
+#define MAX_STATES 100
+#define MAXINT 2147483647
+
+
+char bits_in_16bits [0x1u << 16];
+
+int linkage_disequilibrium;
+
+int borderTol;
+
+int VCF_header_lines;
+char VCF_alignment_name [MAX_CHROM_NAME_VCF];
+int VCF_first_SNP;
+int nxtVCFalignment;
+
+char runName[INFILENAMESIZE];
+
+typedef float cor_t;
+
+
+
+cor_t ABS (cor_t input);
+
+double mainTime0;
+
+int map[INTOKS];
+
+int nofTokens;
+
+int nofSamples;
+
+typedef int al_t;
+typedef double t_sfs;
+
+struct pattern
+{
+ int x;
+ int n;
+ unsigned char f;
+ int c;
+ struct pattern * nxt;
+};
+
+typedef struct
+{
+ al_t *n; // number of valid bases in every site
+ al_t *n_t; // number of valid bases in every site
+ al_t *x; // number of derived bases in every site
+ al_t *x_t; // number of derived bases in every site
+ float * positions;
+ int * positionsInd;
+ int * p_t;
+ unsigned char *folded;
+ unsigned char *f_t;
+ unsigned char userSetFolded;
+ unsigned char userSFS;
+ char* outgroupSequence;
+ char* outgroupName;
+ int outgroupIndex;
+ int sequences;
+ int foldedFormat; // if outgroup exists we set this to zero
+ int segsites;
+ int length;
+
+ int minn;
+ int minx;
+ int maxn;
+ int maxx;
+
+ al_t * stateA;
+ al_t * stateC;
+ al_t * stateG;
+ al_t * stateT;
+
+
+ t_sfs * SFS;
+ t_sfs * tmpSFS;
+ int startSFS;
+ int endSFS;
+
+ int * ng;
+
+ t_sfs * lb;
+ t_sfs * ub;
+
+ int params;
+
+ al_t * n_pat;
+ al_t * x_pat;
+ unsigned char * f_pat;
+ int * c_pat;
+ int patterns;
+
+ t_sfs *** gridProbs;
+ t_sfs * gridADs;
+ t_sfs interval;
+ t_sfs logAD0;
+
+ t_sfs * baseLikelihood;
+
+ struct pattern * patternList;
+
+ float sweepStep;
+
+ int discSites;
+
+#ifdef _USE_PTHREADS
+ t_sfs * threadScoresLIKSFS;
+#endif
+
+} alignment_struct;
+
+alignment_struct * alignment;
+
+double * rv;
+double ** rvLUT;
+double ** rvLUT2;
+
+
+#define GRIDSIZE 300
+#define LOCALGRIDSIZE 100
+
+double div6;
+
+
+typedef struct
+{
+ double * val;
+ int * sc;
+
+} factorial_LUT;
+
+factorial_LUT * factLUT;
+
+
+typedef struct
+{
+
+ int sfRealPos;
+ t_sfs likelihood;
+ t_sfs alpha;
+
+} clr_struct;
+
+clr_struct * clr;
+
+#ifdef _ANALYTICAL_SFS
+typedef struct
+{
+ double t;
+ double d;
+} event;
+
+int eventsTotal;
+event * eventList;
+
+mpfr_t ** analyticalSFS_LUT;
+
+void computeAnalyticalSFS(int sequences, FILE * fp);
+void computeAnalyticalSFSExpo(int sequences, double R, FILE * fpSFSo);
+long double xExponential_Integral_Ei( long double x );
+void mpfr_Exponential_Integral_Ei( mpfr_t EImp, mpfr_t xmp );
+#endif
+
+void printHeading (FILE * fp);
+void computeCorrelationMatrixPairwise(alignment_struct * alignment, clr_struct * omega, int omegaIndex, int firstRowIndex, void * threadData, cor_t ** myCorrelationMatrix, char * lookuptable);
+void applyCorrelationMatrixAdditions (clr_struct * omega, int omegaIndex, int firstRowIndex, cor_t ** correlationMatrix);
+void overlapCorrelationMatrixAdditions (alignment_struct * alignment, clr_struct * omega, int lvw_i, int cvw_i, int * firstRowToCopy, int * firstRowToCompute, int * firstRowToAdd);
+void shiftCorrelationMatrixValues (clr_struct * omega, int lvw_i, int cvw_i, int firstRowToCopy, cor_t ** correlationMatrix);
+
+
+void commandLineParser(int argc, char** argv,
+ char * infile,
+ char * sfsfile,
+ char * sfsofile,
+ char * sfofile,
+ int * grid,
+ int * length,
+ unsigned int * seed,
+ int * fileFormat,
+ int * results,
+ char * outgroupName,
+ unsigned char *userSetFolded,
+ unsigned char * userSFS,
+ unsigned char * onlySFS,
+ unsigned char * onlySF,
+ int * monomorphic,
+ int * threads,
+ int * sequences,
+ int * analyticalSFS,
+ double *growthRate);
+
+void removeMonomorphicSites (int monomorphic, FILE * fp);
+
+t_sfs computeBaseLikelihood();
+t_sfs getAlpha (int sweepPosition, t_sfs * likelihood);
+
+
+int isBinary(char input);
+
+void printIntArray(int *array, int n);
+
+void printUCharArray(unsigned char *array, int n);
+
+void printFloatArray(float *array, int n);
+
+void printCharArray(char *array, int n);
+
+int isEndOfLine(char ent);
+
+void goToLineEnd(FILE *fp);
+
+int findFirstAlignment(FILE *fp, int format);
+
+int findNextAlignment(FILE *fp, int fileFormat);
+
+void freeAlignment();
+
+void readAlignment(FILE *fp, int format, FILE * fpInfo, FILE * sfO);
+
+void compressAlignment(alignment_struct *alignment);
+
+void knuthShuffle(int orgArray[], int arraySize, int start, int end);
+
+int parseSample(FILE *fp, int targetTok, char **word, int *wordLength, int curTok);
+
+void unGetChars(FILE *fp, char* chars, int n);
+
+int isValidDNACharacter(char input);
+
+void parseIndividual(char *word, char** genotype, char delimiter, int token, char* states, char phased, char unphased, int *ploidy, int *max_ploidy);
+
+void ignoreAll(FILE * fp, char * ent);
+
+int isSpace(char ent);
+
+double XchooseY_ln(int x, int y);
+
+void checkSNIPPositions (FILE* fp, alignment_struct * alignment, int index);
+
+void createSFS (FILE * fpSFS, FILE * fpSFSo, int alignmentIndex, int * SFSsize);
+void createCLR (int grid);
+void createPROBS (int probGrid);
+void createPatterns(void);
+void computeFactLUT(void);
+
+double gettime(void);
+
+t_sfs likelihoodSFS_SNP(t_sfs * tmpSFS, int x, int n, unsigned char f, int c);
+
+void updateSF(FILE * fpSFo);
+
+#ifdef _USE_PTHREADS
+
+typedef struct
+{
+ int threadID;
+ int threadTOTAL;
+
+ int threadBARRIER;
+ int threadOPERATION;
+
+}threadData_t;
+
+pthread_t * workerThreadL;
+threadData_t * threadDataL;
+
+int gridP;
+void likelihoodSFS_thread(int tid, int threads);
+void parallelComputationRVLUT_thread(int tid, int threads);
+void computeAlpha_parallel(int grid);
+void parallelComputationAlpha_thread(int tid, int threads);
+void syncThreadsBARRIER();
+
+
+#endif
+
+#ifdef _DO_CHECKPOINTS
+double lastCheckpointTime;
+double checkPointInterval;
+extern void writeCheckpoint();
+#endif
+
+#endif
=====================================
debian/changelog
=====================================
@@ -2,6 +2,7 @@ sweed (3.2.1+dfsg-3) unstable; urgency=medium
* Team upload.
* Add autopkgtests
+ * Correct pristine-tar to generate correct tar
-- Nilesh Patra <npatra974 at gmail.com> Thu, 27 Aug 2020 20:57:35 +0530
View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/da74065873a2199f4d1069655913105bdeeaeb5a...be1ced6a59d674ef750cf301a064f8b303fbcbad
--
View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/da74065873a2199f4d1069655913105bdeeaeb5a...be1ced6a59d674ef750cf301a064f8b303fbcbad
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